If you are on antibiotics (which it sounds like you are because you said your Doc wrote you a script) wait a month or so before you give in your samples. Antibiotics can interfer with the culture results. You dont want any antibiotics in your system for at least a month or so before giving you sample. For instance, if your finish your antibiotics on Jan 25th dont give a sample until Feb 29th!!! You should also wait at least 5 days after you have last ejaculated to give your semen sample, just to make sure you give a nice large healthy amount so they have alot to work with. I didnt ejaculate for 8 days before I gave my sample, just to be safe.

Im sure theres alot to test for, but all I know of are these:

Anaroebic bacterias,
Aroebic bacterias,
The Mycoplasma Group,
Ureaplasma,
STD's like Chlamydia and Gonnorhea,
and Yeast.

Have them test you for the parasite Trichamonas. Doctors seem to neglect this specific parasite even though it is a common STD that causes problems in both males and females alike.

I would request all of this if I were you.
Good Luck and tell us how everything goes.